GIW 2005 The Sixteenth International Conference on Genome Informatics Paci¯co Yokohama, Japan December 19{21, 2005 Scope GIW is the longest running international bioinformatics conference, which provides unique opportu- nities that bridge theory and experiments, academia and industry, and East and West. Its scope includes all work that is ultimately devoted to the computational understanding of biological systems on a molecular basis. Sponsored and Organized by Bioinformatics Center (Kyoto University) Human Genome Center (University of Tokyo) Systems Genomics Towards System-Level Understanding of Life (MEXT of Japan) Japanese Society for Bioinformatics (JSBi) Steering Committee Minoru Kanehisa (Kyoto University) Toshihisa Takagi (University of Tokyo) Satoru Miyano (University of Tokyo) 1 GIW 2005 The Sixteenth International Conference on Genome Informatics Paci¯co Yokohama, Japan December 19{21, 2005 Registration Registration should be done at: http://giw.ims.u-tokyo.ac.jp/giw2005/registration.html un- til December 4, 2005. Registration fee includes a copy of Genome Informatics Vol. 16, No. 2 and co®ee breaks. We o®er registration fee discount for JSBi and ISCB members. until Dec. 4, 2005 after Dec. 4, 2005 Standard JPY15,000.- JPY20,000.- Standard ISCB Member JPY14,000.- JPY19,000.- Registration JSBi Member JPY8,000.- JPY13,000.- JSBi & ISCB Member JPY7,000.- JPY12,000.- Standard JPY10,000.- JPY15,000.- Student ISCB Member JPY9,000.- JPY14,000.- Registration JSBi Member JPY5,000.- JPY10,000.- JSBi & ISCB Member JPY4,000.- JPY9,000.- (Banquet on December 20 evening : JPY6,000.-) Secretary and Local Arrangements Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan Tel: +81-3-5449-5615 / Fax: +81-3-5449-5442 E-mail: [email protected] URL: http://giw.ims.u-tokyo.ac.jp/giw2005/index.html Location The conference will take place at PACIFICO YOKOHAMA. Please get o® at Minato Mirai Station on the Minato Mirai Line (connecting from the Tokyu Toyoko Line). It takes about 3 minutes' walk from the Minato Mirai Station to Paci¯co Yokohama. Address: 1-1-1, Minato Miarai, Nishi-ku, Yokohama 220-0012, Japan Tel: +81-45-221-2155 URL: http://www.pacifico.co.jp/index_e.html Conference Center 2F 3F Posters C9 C2 C4 C7 Entrance GIW 2005 C8 321 C1 C3 C5 C6 Paper Session Registration Commercial Exhibition 12/19䡐21 321 Book Selling Software 321 Demonstrations 311 312 311 315 316 317 313 312 Meeting Internet Internet Room Service Service 313 Me I I n n t t e e w.c. e r r n t n i 31 n 31 31 e e g t t 6 5 7 Ro Ro R o o o o m m m 2 GIW 2005 Advanced Program Registration December 19, 2005: 08:30 - 18:00 December 20, 2005: 08:00 - 18:00 December 21, 2005: 08:00 - 16:00 Monday, December 19, 2005 Opening Address 09:00 - 09:10 Reinhart Heinrich (Humboldt U.) and Hiroshi Mamitsuka(Kyoto U.) Paper Session 1 Chair: Tetsuo Shibuya (U.Tokyo) 09:10 - 09:35 Qualitatively Predicting Acetylation and Methylation Areas in DNA Se- quences, Tho Hoan Pham1, Dang Hung Tran2, Tu Bao Ho2;3, Kenji Satou2;3, Gabriel Valiente4 (1Hanoi U. Pedagogy, 2JAIST, 3JST, 4Technical U. Catalonia) 09:35 - 10:00 Knowledge-Based Prediction of DNA Atomic Structure from Nucleic Se- quence,Marcos J. Ara¶uzo-Bravo, Akinori Sarai (U. Vermont) 10:00 - 10:25 Prediction of Functional Modules Based on Gene Distributions in Micro- bial Genomes, Hongwei Wu1;2, Fenglou Mao1, Zhengchang Su1;2, Victor Olman1, Ying Xu1;2 (1U. Georgia, 2Oak Ridge National Lab.) 10:25: - 11:00 Break Keynote Address Chair: Hiroshi Mamitsuka (Kyoto U.) 11:00 - 12:00 Chemoinformatics, Drug Design, and Systems Biology, Pierre Baldi (UC Irvine) 12:00 - 13:30 Lunch Posters and Software Demonstrations Session 1 13:30 - 14:30 ( Odd Number ) Paper Session 2 Chair: Oliver EbenhÄoh(Humboldt U.) 14:30 - 14:55 Supporting the Curation of Biological Databases with Reusable Text Min- ing, Olivo Miotto1, Tin Wee Tan1, Vladimir Brusic2;3 (1National U. Sin- gapore, 2U. Queensland, 3Inst. for Infocomm Res.) 14:55 - 15:20 Reconstruction of Phylogenetic Relationships from Metabolic Pathways Based on the Enzyme Hierarchy and the Gene Ontology, Jos¶eC. Clemente1, Kenji Satou1, Gabriel Valiente2 (1JAIST, 2Technical U. Catalonia) 15:20 - 15:45 Mass Identi¯cation of Chloroplast Proteins of Endosymbiont Origin by Phylogenetic Pro¯ling Based on Organism-Optimized Homologous Pro- tein Groups, Naoki Sato, Masayuki Ishikawa, Makoto Fujiwara, Kintake Sonoike (U. Tokyo) 15:45: - 16:15 Break Paper Session 3 Chair: Limsoon Wong (Inst.Infocomm Res.) 16:15 - 16:40 Strategies for Genome Reduction in Microbial Genomes, Kishore R. Sakharkar, Vincent T.K. Chow (National U. Singapore) 16:40 - 17:05 Reassembly and Interfacing Neural Models Registered on Biological Model Databases, Mihoko Otake1;2, Toshihisa Takagi1 (1U. Tokyo, 2PRESTO,JST) 3 17:05 - 17:30 Objective Measurement of Spindle Orientation in Early Caenorhabditis el- egans Embryo, Shugo Hamahashi1;2, Shuichi Onami1;2 (1Keio U., 2JST) 17:30 - 17:55 Evolution from Possible Primitive tRNA-Viroids to Early Poly-tRNA- Derived mRNAs: A New Approach from the Poly-tRNA Theory, Koji Ohnishi, Madoka Ohshima, Naotaka Furuichi (Niigata U.) Tuesday, December 20, 2005 Paper Session 4 Chair: Ying Xu (U. Georgia) 09:00 - 09:25 A Study of Fragment-Based Protein Structure Prediction: Biased Frag- ment Replacement for Searching Low-Energy Conformation, Sung-Joon Park (Kobe U.) 09:25 - 09:50 Comparison of Protein Structures by Multi-Objective Optimization, Lu- onan Chen1 Ling-Yun Wu2, Ruiqi Wang1, Yong Wang1 Shihua Zhang2, Xiang-Sun Zhang2 (1Osaka Sangyo U., 2Chinese Acad. of Sci.) 09:50 - 10:15 Statistical Evaluation of a Bottom-Up Clustering for Single Particle Molec- ular Images, Yutaka Ueno1, Katsunori Isono1;2, Katsutoshi Takahashi1, Yukio Shimonohara1;3, Kiyoshi Asai1 (1CBRC, 2INTEC Web and Genome Informatics Corp., 3Information and Mathematical Science Laboratory Inc.) 10:15 - 10:45 Break Paper Session 5 Chair: Koji Tsuda (CBRC) 10:45 - 11:10 Inter-Species Validation for Domain Combination Based Protein-Protein Interaction Prediction Method, Woo-Hyuk Jang 1, Dong-Soo Han 1;3, Hong-Soog Kim 2, Sung-Doke Lee 1 (1Information & Communications U., 2Electronics & Telecommunications Res. Inst., 3Correspondence author) 11:10 - 11:35 A Graph Theoretical Approach for Analysis of Protein Flexibility Change at Protein Complex Formation, Carlos A. Del Carpio M.1, Abdul Rajjak Shaikh1, Eichiro Ichiishi1, Michihisa Koyama1, Momoji Kubo1;2, Kazumi Nishijima1;3, Akira Miyamoto1 (1Tohoku University, 2PRESTO, JST, 3Mochida Pharmaceutical Co. Ltd.) 11:35 - 12:00 A Fast Protein-Protein Docking Algorithm Using Series Expansion in Terms of Spherical Basis Functions, Kazuya Sumikoshi, Tohru Terada, Shugo Nakamura, Kentaro Shimizu (U. Tokyo) 12:00 - 13:30 Lunch Keynote Address Chair: Kenta Nakai (U. Tokyo) 13:30 - 14:30 Membrane Proteins in Vivo and in Silico: Getting the Best of Two Worlds, Gunnar von Heijne (Stockholm U.) Paper Session 6 Chair: Gabriel Valiente (Tech. U. Catalonia) 14:30 - 14:55 Viewing the Proteome from Oligopeptides and Prediction of Protein Func- tion, Hisayuki Horai1;2, Kouichi Doi1, Hirofumi Doi1;2 (1NAIST, 2Celestar Lexico-Sciences, Inc.) 14:55 - 15:20 Mass Distributed Clustering: A New Algorithm for Repeated Measure- ments in Gene Expression Data, Shinya Matsumoto1, Ken-ichi Aisaki2, Jun Kanno2 (1NCR Japan, Ltd., 2NIHS) 4 15:20 - 15:45 Diagnosis of Early Relapse in Ovarian Cancer Using Serum Proteomic Pro- ¯ling, Jung Hun Oh1, Jean Gao1, Animesh Nandi2, Prem Gurnani2, Lynne Knowles3, John Schorge3, Kevin P. Rosenblatt2 (1U.Texas, 2UT Southwest- ern Med. Center, Dallas) 15:45: - 16:00 Break JSBi Annual Meeting 16:00 - 16:30 Posters and Software Demonstrations Session 2 16:30 - 18:00 ( Even Number ) Banquet 18:30 - 20:30 Ballroom \Monaco" at Inter Continental The Grand Yokohama Wednesday, December 21, 2005 Paper Session 7 Chair: Tatsuya Akutsu (Kyoto U.) 09:00 - 09:25 Reverse Engineering Genetic Networks Using Evolutionary Computation, Nasimul Noman, Hitoshi Iba (U. Tokyo) 09:25 - 09:50 Toward Integration of Systems Biology Formalism: The Gene Regulatory Networks Case, Ra®aella Gentilini (U. Udine) 09:50 - 10:15 Reconstruction of Gene Regulatory Networks under the Finite State Linear Model, Dace Ruklisa1, Alvis Brazma2, Juris Viksna1 (1U. Latvia, 2EBI) 10:15 - 10:40 A Space-E±cient Algorithm for the Constrained Pairwise Sequence Align- ment Problem, Dan He, Abdullah N. Arslan (U. Vermont) Posters and Software Demonstrations Session 3 10:40 - 12:00 12:00 - 13:30 Lunch Keynote Address Chair: Reinhart Heinrich (Humboldt U.) 13:30 - 14:30 Cell-Cell Interaction Network That Generates the Skin Pattern of Animal, Shigeru Kondo (Nagoya U.) Paper Session 8 Chair: 14:30 - 14:55 Automatic Drawing of Biological Networks Using Cross Cost and Subcom- ponent Data, Mitsuru Kato, Masao Nagasaki, Atsushi Doi, Satoru Miyano (U. Tokyo) 14:55 - 15:20 Interaction Graph Mining for Protein Complexes Using Local Clique Merg- ing, Xiao-Li Li1, Soon-Heng Tan1;2, Chuan-Sheng Foo1;3, See-Kiong Ng1 (1Inst. for Infocomm Res., 2National U. Singapore, 3Stanford U.) 15:20 - 15:45 Topology of Mammalian Transcription Networks, Anatolij P. Potapov1, Nico Voss2, Nicole Sasse1, Edgar Wingender1;2 (1U. GÄottingen, 2BIOBASE GmbH) Closing and Award Ceremony 15:45 - 16:00 5 Commercial Exhibitions C1: Ryoka Systems Inc. C2: CTC Laboratory Systems Corporation C3: NABE International Corporation C4: SGI Japan, Ltd. C5: Mathematical Systems, Inc. C6: Pathway Solutions Inc. C7: HITACHI,